Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus.

Jose De Vega,Sarah Dyer,Iain Donnison,Kerrie Farrar

doi:10.12688/f1000research.44714.1

Abstract

Miscanthus sacchariflorus (Maxim.) Hack. is a highly productive C4 perennial rhizomatous biofuel grass crop. M. sacchariflorus is among the most widely distributed species in the genus, particularly at cold northern latitudes, and is one of the progenitor species of the commercial M.×giganteus genotypes. We generated a 2.54 Gb whole-genome assembly of the diploid M. sacchariflorus cv. "Robustus 297" genotype, which represented ~59% of the expected total genome size. We later anchored this assembly using the chromosomes from the M. sinensis genome to generate a second assembly with improved contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored assemblies, respectively. We estimated our assemblies included ~85% of the M. sacchariflorus genes based on homology and core markers. The utility of the new reference for genomic studies was evidenced by a 99% alignment rate of the RNA-seq reads from the same genotype. The raw data, unanchored and anchored assemblies, and respective gene annotations are publicly available.

Highlights

Miscanthus is a genus of C4 perennial rhizomatous grasses native to East Asia and Oceania, and naturally adapted to a wide range of climate zones and land types
M. x giganteus, a sterile triploid hybrid resulting from the hybridization between M. sinensis and M. sacchariflorus, is the predominant commercially grown species owing to its high biomass productivity and low chemical input requirements
The repeats annotation was deposited in Zenodo (See data availability); (2) exon-intron junctions identified by Tophat[13]; (3) de novo and genome-guided ab initio transcripts assembled with Trinity14and Cufflinks[15] from RNA-Seq reads obtained from several tissues from the same genotype; (4) ab initio gene models predicted by SNAP16 and GeneID17; and (5) homology-based alignments of transcripts and proteins from Miscanthus sinensis and maize using Exonerate[18] with a minimal identity of 0.7 and coverage of 0.7

Summary

Introduction

Miscanthus is a genus of C4 perennial rhizomatous grasses native to East Asia and Oceania, and naturally adapted to a wide range of climate zones and land types. We obtained 589K scaffolds, a total length of 2.54 Gb with an N50 of 10.2 Kb. This whole-genome assembly was denominated “Msac_v2” and is deposited at NCBI in BioProject PRJNA679435.

Results

Conclusion